tbuckley/cabot-search huggingface dataset:
A survey on clinical natural language processing in the United Kingdom from 2007 to 2022
Authors: Honghan Wu, Minhong Wang, Jinge Wu, Farah Francis, Yun-Hsuan Chang, Alex Shavick, Hang Dong, Michael T. C. Poon, Natalie Fitzpatrick, Adam P. Levine, Luke T. Slater, Alex Handy, Andreas Karwath, Georgios V. Gkoutos, Claude Chelala, Anoop Dinesh Shah, Robert Stewart, Nigel Collier, Beatrice Alex, William Whiteley, Cathie Sudlow, Angus Roberts, Richard J. B. Dobson
Journal: npj Digital Medicine (2022)

Much of the knowledge and information needed for enabling high-quality clinical research is stored in free-text format. Natural language processing (NLP) has been used to extract information from these sources at scale for several decades. This paper aims to present a comprehensive review of clinical NLP for the past 15 years in the UK to identify the community, depict its evolution, analyse methodologies and applications, and identify the main barriers. We collect a dataset of clinical NLP projects (n = 94; £ = 41.97 m) funded by UK funders or the European Union's funding programmes. Additionally, we extract details on 9 funders, 137 organisations, 139 persons and 431 research papers. Networks are created from timestamped data interlinking all entities, and network analysis is subsequently applied to generate insights. 431 publications are identified as part of a literature review, of which 107 are eligible for final analysis. Results show, not surprisingly, clinical NLP in the UK has increased substantially in the last 15 years: the total budget in the period of 2019-2022 was 80 times that of 2007-2010. However, the effort is required to deepen areas such as disease (sub-)phenotyping and broaden application domains. There is also a need to improve links between academia and industry and enable deployments in real-world settings for the realisation of clinical NLP's great potential in care delivery. The major barriers include research and development access to hospital data, lack of capable computational resources in the right places, the scarcity of labelled data and barriers to sharing of pretrained models.
GDNF‐Loaded Polydopamine Nanoparticles‐Based Anisotropic Scaffolds Promote Spinal Cord Repair by Modulating Inhibitory Microenvironment
Authors: Jinjin Ma, Jiaying Li, Xingran Wang, Meimei Li, Wenwen Teng, Zihan Tao, Jile Xie, Yanxia Ma, Qin Shi, Bin Li, None Saijilafu
Journal: Advanced Healthcare Materials (2022)

Abstract Spinal cord injury (SCI) is a devastating injury that causes permanent loss of sensation and motor function. SCI repair is a significant challenge due to the limited regenerating ability of adult neurons and the complex inflammatory microenvironment. After SCI, the oxidative stress induced by excessive reactive oxygen species (ROS) often leads to prolonged neuroinflammation that results in sustained damage to the spinal cord tissue. Polydopamine (PDA) shows remarkable capability in scavenging ROS to treat numerous inflammatory diseases. In this study, glial cell‐derived neurotrophic factor (GDNF)‐loaded PDA nanoparticle‐based anisotropic scaffolds for spinal cord repair are developed. It is found that mesoporous PDA nanoparticles (mPDA NPs) in the scaffolds efficiently scavenge ROS and promote microglia M2 polarization, thereby inhibiting inflammatory response at the injury site and providing a favorable microenvironment for nerve cell survival. Furthermore, the GDNF encapsulated in mPDA NPs promotes corticospinal tract motor axon regeneration and its locomotor functional recovery. Together, findings from this study reveal that the GDNF‐loaded PDA/Gelatin scaffolds hold potential as an effective artificial transplantation material for SCI treatment.
Comment on: Combination therapy with long-acting bronchodilators and the risk of major adverse cardiovascular events in patients with COPD: a systematic review and meta-analysis
Authors: Pere Almagro, Pablo Martinez-Camblor
Journal: European Respiratory Journal (2022)

We read with great interest the meta-analysis recently published in the European Respiratory Journal by Yang et al. [1] concerning the risk of major adverse cardiovascular events (MACE) in COPD patients with dual bronchodilatation (long-acting β2 agonist (LABA)/long-acting muscarinic antagonist (LAMA)) or triple therapy (LABA/LAMA/inhaled corticosteroids (ICS)) compared with LABA/ICS. COPD patients had an increased cardiovascular risk. The impact of triple therapy on cardiovascular events is controversial compared to its clinical benefits. <https://bit.ly/3OSRTmZ>
FANAZymes: A new class of nucleic acid enzymes
Authors: John J. Rossi
Journal: Molecular Therapy (2022)

In recent years, there has been diminished interest in nucleic acid enzymes. However, Taylor and colleagues' new study on 2′-deoxy-2′-fluoro-β-d-arabino nucleic acids (FANAs) in Nature Chemistry may thrust these enzymes back into the spotlight. 1 Taylor A.I. Wan C.J.K. Donde M.J. Peak-Chew S.Y. Holliger P. A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing. Nat. Chem. 2022; 14: 1295-1305https://doi.org/10.1038/s41557-022-01021-z Crossref PubMed Scopus (12) Google Scholar Indeed, the Nobel prize-winning discovery that RNA can function as a site-specific RNA-cleaving enzyme by Cech, Altman, and colleagues (reviewed in Rossi 2 Rossi J.J. Ribozymes, genomics and therapeutics. Chem. Biol. 1999; 6: R33-R37https://doi.org/10.1016/S1074-5521(99)80001-5 Abstract Full Text PDF PubMed Scopus (63) Google Scholar ) prompted a flurry of investigations into ribozymes and their function. One critical advancement in this field was the discovery of the hammerhead ribozyme, a plant viroid RNA self-cleaving motif that functions by Watson-Crick base pairing flanking the GUC cleavage site. 2 Rossi J.J. Ribozymes, genomics and therapeutics. Chem. Biol. 1999; 6: R33-R37https://doi.org/10.1016/S1074-5521(99)80001-5 Abstract Full Text PDF PubMed Scopus (63) Google Scholar ,3 Forster A.C. Symons R.H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell. 1987; 49: 211-220https://doi.org/10.1016/0092-8674(87)90562-9 Abstract Full Text PDF PubMed Scopus (569) Google Scholar ,4 Haseloff J. Gerlach W.L. Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature. 1988; 334: 585-591https://doi.org/10.1038/334585a0 Crossref PubMed Scopus (970) Google Scholar The therapeutic application of hammerhead ribozyme was quickly realized because it can function in trans to cleave any complementary target transcript, thereby destroying the transcript function. 4 Haseloff J. Gerlach W.L. Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature. 1988; 334: 585-591https://doi.org/10.1038/334585a0 Crossref PubMed Scopus (970) Google Scholar
Consent Laws for Minors Regarding Sexually Transmitted Infection and HIV Services—Reply
Authors: Kristen Underhill, Kimberly M. Nelson
Journal: JAMA (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Deep learning based on preoperative magnetic resonance (MR) images improves the predictive power of survival models in primary spinal cord astrocytomas
Authors: Ting Sun, Yongzhi Wang, Xing Liu, Zhaohui Li, Jie Zhang, Jing Lu, Liying Qu, Sven Haller, Yunyun Duan, Zhizheng Zhuo, Dan Cheng, Xiaolu Xu, Wenqing Jia, Yaou Liu
Journal: Neuro-Oncology (2022)

Prognostic models for spinal cord astrocytoma patients are lacking due to the low incidence of the disease. Here, we aim to develop a fully automated deep learning (DL) pipeline for stratified overall survival (OS) prediction based on preoperative MR images.A total of 587 patients diagnosed with intramedullary tumors were retrospectively enrolled in our hospital to develop an automated pipeline for tumor segmentation and OS prediction. The automated pipeline included a T2WI-based tumor segmentation model and 3 cascaded binary OS prediction models (1-year, 3-year, and 5-year models). For the tumor segmentation model, 439 cases of intramedullary tumors were used to model training and testing using a transfer learning strategy. A total of 138 patients diagnosed with astrocytomas were included to train and test the OS prediction models via 10 × 10-fold cross-validation using CNNs.The dice of the tumor segmentation model with the test set was 0.852. The results indicated that the best input of OS prediction models was a combination of T2W and T1C images and the tumor mask. The 1-year, 3-year, and 5-year automated OS prediction models achieved accuracies of 86.0%, 84.0%, and 88.0% and AUCs of 0.881 (95% CI 0.839-0.918), 0.862 (95% CI 0.827-0.901), and 0.905 (95% CI 0.867-0.942), respectively. The automated DL pipeline achieved 4-class OS prediction (<1 year, 1-3 years, 3-5 years, and >5 years) with 75.3% accuracy.We proposed an automated DL pipeline for segmenting spinal cord astrocytomas and stratifying OS based on preoperative MR images.
Comparison of US Firearm-Related Deaths Among Children and Adolescents by Race and Ethnicity, 1999-2020
Authors: Leonardo Mariño-Ramírez, I. King Jordan, Anna María Nápoles, Eliseo J. Pérez-Stable
Journal: JAMA (2022)

This study assesses racial and ethnic differences in overall burden of firearm-related mortality and in change in firearm-related mortality among youths from 1999 to 2020.
The transmission of pottery technology among prehistoric European hunter-gatherers
Authors: Ekaterina Dolbunova, Alexandre Lucquin, T. Rowan McLaughlin, Manon Bondetti, Blandine Courel, Ester Oras, Henny Piezonka, Harry K. Robson, Helen Talbot, Kamil Adamczak, Konstantin Andreev, Vitali Asheichyk, Maxim Charniauski, Agnieszka Czekaj-Zastawny, Igor Ezepenko, Tatjana Grechkina, Alise Gunnarssone, Tatyana M. Gusentsova, Dmytro Haskevych, Marina Ivanischeva, Jacek Kabaciński, Viktor Karmanov, Natalia Kosorukova, Elena Kostyleva, Aivar Kriiska, Stanisław Kukawka, Olga Lozovskaya, Andrey Mazurkevich, Nadezhda Nedomolkina, Gytis Piličiauskas, Galina Sinitsyna, Andrey Skorobogatov, Roman V. Smolyaninov, Aleksey Surkov, Oleg Tkachov, Maryia Tkachova, Andrey Tsybrij, Viktor Tsybrij, Aleksandr A. Vybornov, Adam Wawrusiewicz, Aleksandr I. Yudin, John Meadows, Carl Heron, Oliver E. Craig
Journal: Nature Human Behaviour (2022)

Abstract Human history has been shaped by global dispersals of technologies, although understanding of what enabled these processes is limited. Here, we explore the behavioural mechanisms that led to the emergence of pottery among hunter-gatherer communities in Europe during the mid-Holocene. Through radiocarbon dating, we propose this dispersal occurred at a far faster rate than previously thought. Chemical characterization of organic residues shows that European hunter-gatherer pottery had a function structured around regional culinary practices rather than environmental factors. Analysis of the forms, decoration and technological choices suggests that knowledge of pottery spread through a process of cultural transmission. We demonstrate a correlation between the physical properties of pots and how they were used, reflecting social traditions inherited by successive generations of hunter-gatherers. Taken together the evidence supports kinship-driven, super-regional communication networks that existed long before other major innovations such as agriculture, writing, urbanism or metallurgy.
Persistent post–COVID-19 smell loss is associated with immune cell infiltration and altered gene expression in olfactory epithelium
Authors: John B. Finlay, David H. Brann, Ralph Abi Hachem, David W. Jang, Allison D. Oliva, Tiffany Ko, Rupali Gupta, Sebastian A. Wellford, E. Ashley Moseman, Sophie S. Jang, Carol H. Yan, Hiroaki Matsunami, Tatsuya Tsukahara, Sandeep Robert Datta, Bradley J. Goldstein
Journal: Science Translational Medicine (2022)

SARS-CoV-2 causes profound changes in the sense of smell, including total smell loss. Although these alterations are often transient, many patients with COVID-19 exhibit olfactory dysfunction that lasts months to years. Although animal and human autopsy studies have suggested mechanisms driving acute anosmia, it remains unclear how SARS-CoV-2 causes persistent smell loss in a subset of patients. To address this question, we analyzed olfactory epithelial samples collected from 24 biopsies, including from nine patients with objectively quantified long-term smell loss after COVID-19. This biopsy-based approach revealed a diffuse infiltrate of T cells expressing interferon-γ and a shift in myeloid cell population composition, including enrichment of CD207+ dendritic cells and depletion of anti-inflammatory M2 macrophages. Despite the absence of detectable SARS-CoV-2 RNA or protein, gene expression in the barrier supporting cells of the olfactory epithelium, termed sustentacular cells, appeared to reflect a response to ongoing inflammatory signaling, which was accompanied by a reduction in the number of olfactory sensory neurons relative to olfactory epithelial sustentacular cells. These findings indicate that T cell-mediated inflammation persists in the olfactory epithelium long after SARS-CoV-2 has been eliminated from the tissue, suggesting a mechanism for long-term post-COVID-19 smell loss.
Interstitial lung disease progression after genomic usual interstitial pneumonia testing
Authors: Sachin Chaudhary, S. Sam Weigt, Manuel L. Ribeiro Neto, Bryan S. Benn, Janelle Vu Pugashetti, Rebecca Keith, Arista Chand, Scott Oh, Fayez Kheir, Vijaya Ramalingam, Joshua J. Solomon, Richart Harper, Joseph A. Lasky, Justin M. Oldham
Journal: European Respiratory Journal (2022)

Background A genomic classifier for usual interstitial pneumonia (gUIP) has been shown to predict histological UIP with high specificity, increasing diagnostic confidence for idiopathic pulmonary fibrosis (IPF). Whether those with positive gUIP classification exhibit a progressive, IPF-like phenotype remains unknown. Methods A pooled, retrospective analysis of patients who underwent clinically indicated diagnostic bronchoscopy with gUIP testing at seven academic medical centres across the USA was performed. We assessed the association between gUIP classification and 18-month progression-free survival (PFS) using Cox proportional hazards regression. PFS was defined as the time from gUIP testing to death from any cause, lung transplant, ≥10% relative decline in forced vital capacity (FVC) or censoring at the time of last available FVC measure. Longitudinal change in FVC was then compared between gUIP classification groups using a joint regression model. Results Of 238 consecutive patients who underwent gUIP testing, 192 had available follow-up data and were included in the analysis, including 104 with positive gUIP classification and 88 with negative classification. In multivariable analysis, positive gUIP classification was associated with reduced PFS (hazard ratio 1.58, 95% CI 0.86–2.92; p=0.14), but this did not reach statistical significance. Mean annual change in FVC was −101.8 mL (95% CI −142.7– −60.9 mL; p&lt;0.001) for those with positive gUIP classification and −73.2 mL (95% CI −115.2– −31.1 mL; p&lt;0.001) for those with negative classification (difference 28.7 mL, 95% CI −83.2–25.9 mL; p=0.30). Conclusions gUIP classification was not associated with differential rates of PFS or longitudinal FVC decline in a multicentre interstitial lung disease cohort undergoing bronchoscopy as part of the diagnostic evaluation.
Monkeypox Virus Infection across 16 Countries — April–June 2022
Authors: John P Thornhill, Andrea Antinori, Chloe M Orkin
Journal: New England Journal of Medicine (2022)

To the Editor: According to Thornhill et al. (Aug.25 issue), 1 semen was positive for monkeypox (recently renamed mpox) virus on polymerase-chain-reaction testing in 29 persons.Did the authors analyze prostatic fluid?Semen is not homogeneous and results from at least four exocrine organs and four mucosal exocrine glands.The majority of human immunodeficiency virus (HIV) in semen originates distal to the vas deferens. 2The importance of the prostate reservoir for HIV was shown by Smith et al., who found undetectable seminal plasma HIV RNA in all semen samples obtained without prostatic massage but detectable seminal plasma HIV RNA (≥25 copies per milliliter) in at least one sample obtained after prostatic massage. 3Detailed localization studies of mpox virus are important because the prostate may serve as a reservoir and mpox virus may arise from local replication in the male genitourinary subcompartments.Second, did the authors observe Trichomonas vaginalis in any of the persons infected with mpox virus?Although T. vaginalis infection is not necessarily a reportable condition, it has been implicated in the pathogenesis of persistent urethritis and prostatitis owing to the postulated phagocytosis and potential killing of Neisseria gonorrhoeae. 4T. vaginalis may be an important endocytobiotic agent in the transmission and potential persistence of mpox virus infection in the genitourinary tract.
Anti-PEG antibodies before and after a first dose of Comirnaty® (mRNA-LNP-based SARS-CoV-2 vaccine)
Authors: Yaelle Bavli, Bing-Mae Chen, Guy Gross, Alon Hershko, Keren Turjeman, Steve Roffler, Yechezkel Barenholz
Journal: Journal of Controlled Release (2023)
Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease
Authors: Yijun Zhu, Mohammed Dwidar, Ina Nemet, Jennifer A. Buffa, Naseer Sangwan, Xinmin S. Li, James T. Anderson, Kymberleigh A. Romano, Xiaoming Fu, Masanori Funabashi, Zeneng Wang, Pooja Keranahalli, Shawna Battle, Aaron N. Tittle, Adeline M. Hajjar, Valentin Gogonea, Michael A. Fischbach, Joseph A. DiDonato, Stanley L. Hazen
Journal: Cell Host & Microbe (2022)
Enhancing the success of IVF with artificial intelligence
Authors: None The Lancet Digital Health
Journal: The Lancet Digital Health (2022)

The new year brings hope for new beginnings, perhaps the most pertinent of which is new life. For decades, in-vitro fertilisation (IVF) has offered those unable to conceive naturally the chance to have biological children; however, global success rates are notoriously low. Artificial intelligence (AI) is being used to improve the success rates of IVF, but it is not without its challenges. Does AI have the potential to be a clinically useful tool to increase the success of IVF?
Prognostic impact of the AML ELN2022 risk classification in patients undergoing allogeneic stem cell transplantation
Authors: Madlen Jentzsch, Lara Bischof, Jule Ussmann, Donata Backhaus, Dominic Brauer, Klaus H. Metzeler, Maximilian Merz, Vladan Vucinic, Georg-Nikolaus Franke, Marco Herling, Uwe Platzbecker, Sebastian Schwind
Journal: Blood Cancer Journal (2022)

For most patients with acute myeloid leukemia (AML), an allogeneic hematopoietic stem cell transplantation (HSCT) offers the highest chance of cure. Recently, the European LeukemiaNet (ELN) published updated recommendations on the diagnosis and risk classification in AML based on genetic factors at diagnosis as well as a dynamic adjustment (reclassification) according to the measurable residual disease (MRD) status for the favorable and intermediate risk groups. Validation of the ELN2022 risk classification has not been reported. We retrospectively analyzed 522 AML patients who received an HSCT at a median age of 59 (range 16-76) years. For patients with adequate material available and in remission prior to HSCT (n = 229), the MRD status was evaluated. Median follow-up after HSCT was 3.0 years. ELN2022 risk at diagnosis was in 22% favorable, in 26% intermediate, and in 52% adverse. ELN2022 risk at diagnosis is associated with the cumulative incidence of relapse/progression (CIR), event-free survival (EFS), and overall survival (OS) in the whole patient cohort, as well as the subgroup of patients transplanted in first remission. However, the risk stratification based on the ELN2022 classification did not significantly improve outcome prognostication in comparison to the ELN2017 classification. In our study, the newly added group of patients with myelodysplasia-related gene mutations did not have adverse outcomes. Re-classifying these patients into the intermediate risk group and adjusting the grouping for all AML patients by MRD at HSCT, led to a refined and improved risk stratification, which should be validated in independent studies.
A non-invasive artificial intelligence approach for the prediction of human blastocyst ploidy: a retrospective model development and validation study
Authors: Josue Barnes, Matthew Brendel, Vianne R Gao, Suraj Rajendran, Junbum Kim, Qianzi Li, Jonas E Malmsten, Jose T Sierra, Pantelis Zisimopoulos, Alexandros Sigaras, Pegah Khosravi, Marcos Meseguer, Qiansheng Zhan, Zev Rosenwaks, Olivier Elemento, Nikica Zaninovic, Iman Hajirasouliha
Journal: The Lancet Digital Health (2022)
Sulfotransferase 2B1b, Sterol Sulfonation, and Disease
Authors: Ian Cook, Thomas S. Leyh
Journal: Pharmacological Reviews (2022)

The primary function of human sulfotransferase 2B1b (SULT2B1b) is to sulfonate cholesterol and closely related sterols. SULT2B1b sterols perform a number of essential cellular functions. Many are signaling molecules whose activities are redefined by sulfonation—allosteric properties are switched "on" or "off," agonists are transformed into antagonists, and vice versa. Sterol sulfonation is tightly coupled to cholesterol homeostasis, and sulfonation imbalances are causally linked to cholesterol-related diseases including certain cancers, Alzheimer disease, and recessive X-linked ichthyosis—an orphan skin disease. Numerous studies link SULT2B1b activity to disease-relevant molecular processes. Here, these multifaceted processes are integrated into metabolic maps that highlight their interdependence and how their actions are regulated and coordinated by SULT2B1b oxysterol sulfonation. The maps help explain why SULT2B1b inhibition arrests the growth of certain cancers and make the novel prediction that SULT2B1b inhibition will suppress production of amyloid <i>β</i> (A<i>β</i>) plaques and tau fibrils while simultaneously stimulating A<i>β</i> plaque phagocytosis. SULT2B1b harbors a sterol-selective allosteric site whose structure is discussed as a template for creating inhibitors to regulate SULT2B1b and its associated biology. <h3>Significance Statement</h3> Human sulfotransferase 2B1b (SULT2B1b) produces sterol-sulfate signaling molecules that maintain the homeostasis of otherwise pro-disease processes in cancer, Alzheimer disease, and X-linked ichthyosis—an orphan skin disease. The functions of sterol sulfates in each disease are considered and codified into metabolic maps that explain the interdependencies of the sterol-regulated networks and their coordinate regulation by SULT2B1b. The structure of the SULT2B1b sterol-sensing allosteric site is discussed as a means of controlling sterol sulfate biology.